CCP14 Homepage - Single Crystal and Powder Diffraction - Methods, Problems and Solutions - Restrained Rietveld Structure Refinement of Organics - Using Crystals Generated Restraints Commands for Restrained Refinement in Fullprof

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CCP14

Methods, Problems and Solutions

Restrained Rietveld Structure Refinement of Organics

Using Crystals Generated Restraints Commands for Restrained Refinement in Fullprof

(Not including hydrogen placement)

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Back to Problems and Solutions] | [Back to Restrained Rietveld Refinement of Organics Page]| [Back to Fullprof Tutorials Page]

The following will go through converting the Crystals restraints list into Fullprof format, inputting this into GSAS format; then performing the restrained refinement.
(Refer to the CCP14 Based Fullprof Tutorial Pages for download information on Fullprof)
At present (October 2000), converting the Crystals restraints list is done manually and only bond-restraints are supported by Fullprof (no bond-angle restraints/planar restraints).
Again, it is important that the restraint commands you generated in Crystals matches the atom labels in Fullprof or mayhem and chaos will result.
Also refer to Randomly Perturbing Atomic Positions in Crystals. This can be relevant for successfully performing DLS and refinement involving pseudo-symmetry.

Crystals Restraints List from previous tutorial page

DIST   1.352,.01= O(2) TO C(12) 
DIST   1.432,.01= O(3) TO C(17) 
DIST   1.259,.01= O(4) TO C(22) 
DIST   1.234,.01= O(5) TO C(24) 
DIST   1.422,.01= O(6) TO C(25) 
DIST   1.330,.01= O(7) TO C(26) 
DIST   1.276,.01= O(8) TO C(28) 
DIST   1.313,.01= O(9) TO C(30) 
DIST   1.494,.01= N(10) TO C(21) 
DIST   1.490,.01= N(10) TO C(32) 
DIST   1.491,.01= N(10) TO C(33) 
DIST   1.301,.01= N(11) TO C(30) 
DIST   1.386,.01= C(12) TO C(13) 
DIST   1.405,.01= C(12) TO C(29) 
DIST   1.357,.01= C(13) TO C(14) 
DIST   1.399,.01= C(14) TO C(15) 
DIST   1.375,.01= C(15) TO C(16) 
DIST   1.534,.01= C(16) TO C(17) 
DIST   1.422,.01= C(16) TO C(29) 
DIST   1.540,.01= C(17) TO C(18) 
DIST   1.516,.01= C(17) TO C(31) 
DIST   1.526,.01= C(18) TO C(19) 
DIST   1.512,.01= C(18) TO C(27) 
DIST   1.534,.01= C(19) TO C(20) 
DIST   1.538,.01= C(20) TO C(21) 
DIST   1.522,.01= C(20) TO C(25) 
DIST   1.522,.01= C(21) TO C(22) 
DIST   1.403,.01= C(22) TO C(23) 
DIST   1.427,.01= C(23) TO C(24) 
DIST   1.435,.01= C(23) TO C(30) 
DIST   1.552,.01= C(24) TO C(25) 
DIST   1.508,.01= C(25) TO C(26) 
DIST   1.354,.01= C(26) TO C(27) 
DIST   1.445,.01= C(27) TO C(28) 
DIST   1.451,.01= C(28) TO C(29)

Restraints in Fullprof Format

The Fullprof dis parameter (to the right of the number of atoms in the phase) is set to the number of restraints, in this case "35".

O2   C12    1    0.00000    0.00000    0.00000    1.35200    0.01000
O3   C17    1    0.00000    0.00000    0.00000    1.43200    0.01000
O4   C22    1    0.00000    0.00000    0.00000    1.25900    0.01000
O5   C24    1    0.00000    0.00000    0.00000    1.23400    0.01000
O6   C25    1    0.00000    0.00000    0.00000    1.42200    0.01000
O7   C26    1    0.00000    0.00000    0.00000    1.33000    0.01000
O8   C28    1    0.00000    0.00000    0.00000    1.27600    0.01000
O9   C30    1    0.00000    0.00000    0.00000    1.31300    0.01000
N10  C21    1    0.00000    0.00000    0.00000    1.49400    0.01000
N10  C32    1    0.00000    0.00000    0.00000    1.49000    0.01000
N10  C33    1    0.00000    0.00000    0.00000    1.49100    0.01000
N11  C30    1    0.00000    0.00000    0.00000    1.30100    0.01000
C12  C13    1    0.00000    0.00000    0.00000    1.38600    0.01000
C12  C29    1    0.00000    0.00000    0.00000    1.40500    0.01000
C13  C14    1    0.00000    0.00000    0.00000    1.35700    0.01000
C14  C15    1    0.00000    0.00000    0.00000    1.39900    0.01000
C15  C16    1    0.00000    0.00000    0.00000    1.37500    0.01000
C16  C17    1    0.00000    0.00000    0.00000    1.53400    0.01000
C16  C29    1    0.00000    0.00000    0.00000    1.42200    0.01000
C17  C18    1    0.00000    0.00000    0.00000    1.54000    0.01000
C17  C31    1    0.00000    0.00000    0.00000    1.51600    0.01000
C18  C19    1    0.00000    0.00000    0.00000    1.52600    0.01000
C18  C27    1    0.00000    0.00000    0.00000    1.51200    0.01000
C19  C20    1    0.00000    0.00000    0.00000    1.53400    0.01000
C20  C21    1    0.00000    0.00000    0.00000    1.53800    0.01000
C20  C25    1    0.00000    0.00000    0.00000    1.52200    0.01000
C21  C22    1    0.00000    0.00000    0.00000    1.52200    0.01000
C22  C23    1    0.00000    0.00000    0.00000    1.40300    0.01000
C23  C24    1    0.00000    0.00000    0.00000    1.42700    0.01000
C23  C30    1    0.00000    0.00000    0.00000    1.43500    0.01000
C24  C25    1    0.00000    0.00000    0.00000    1.55200    0.01000
C25  C26    1    0.00000    0.00000    0.00000    1.50800    0.01000
C26  C27    1    0.00000    0.00000    0.00000    1.35400    0.01000
C27  C28    1    0.00000    0.00000    0.00000    1.44500    0.01000
C28  C29    1    0.00000    0.00000    0.00000    1.45100    0.01000

Fullprof Input File

(For comparison with single crystal results of tetracycline refer: "Tetracycline hydrochloride: a synchrotron micro-crystal study" Clegg W. & Teat S.J. Acta Cryst., C56 , 1343-1345 (2000))

Paste the restraints into the Fullprof file.

COMM  Tetracycline C22H24N2O8HCl  P212121                           
! Files => DAT-file: refine,  PCR-file: refine
!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
   0   5   1  26   0   0   1   1   0   0   1   0   0   0   0   0   0   0   0
!
!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana
   0   0   1   0   1   0   0   0   1   1   0   1   0   1   2   0   0
!
! lambda1 Lambda2    Ratio   Bkpos    Wdt    Cthm     muR   AsyLim   Rpolarz ->Patt# 1
 1.540560 1.544390  0.5000 90.0000 12.0000  0.7998  0.0000   34.50    0.5000
!
!NCY  Eps  R_at  R_an  R_pr  R_gl     Thmin       Step       Thmax    PSD    Sent0
  9  0.01  0.50  0.50  0.50  0.50      7.0000     0.0200   100.0000   0.000   0.000
!
!2Theta/TOF/E(Kev)   Background  for Pattern#  1
        6.850     3035.166
        7.917     2648.353
       12.312     1826.374
       14.258     1729.671
       17.209     1584.617
       18.967     1584.617
       25.496     1536.266
       29.639     1778.023
       34.347     1923.077
       38.428     1778.023
       45.208     1923.077
       47.092     1729.671
       50.725     1550.550
       56.585     1110.989
       58.343     1005.495
       61.356      970.330
       64.453      952.748
       69.057      882.418
       73.158      864.836
       78.097      847.253
       80.859      847.253
       84.877      864.836
       87.640      759.341
       91.490      636.264
       94.922      636.264
      100.279      565.935
! 
!
     104    !Number of refined parameters
!
!  Zero    Code    Sycos    Code   Sysin    Code  Lambda     Code MORE ->Patt# 1
 -0.08755   0.00  0.00000   0.00  0.00000   0.00 0.000000    0.00   0
!-------------------------------------------------------------------------------
!  Data for PHASE number:   1  ==> Current R_Bragg for Pattern#  1:    19.39
!-------------------------------------------------------------------------------
 C22H24N2O8HCl                                                                  
!
!Nat Dis Mom Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth     ATZ   Nvk Npr More
  33  35   0 1.0 0.0 0.0   0   0   0   0   0        0.00   0   5   0
!
P 21 21 21               <--Space group symbol
!Atom Typ       X        Y        Z     Biso      Occ     In Fin N_t Poi /Codes
Cl1  CL      0.92697  0.42257 -0.00119  2.34344  1.00000   0   0   0    0
               21.00    31.00    41.00    51.00     0.00
O2   O       0.01188  0.37313  0.43554  2.90609  1.00000   0   0   0    0
               61.00    71.00    81.00  1031.00     0.00
O3   O       0.14336  0.45564  0.12582  2.90609  1.00000   0   0   0    0
               91.00   101.00   111.00  1031.00     0.00
O4   O       0.75524  0.64890  0.07187  2.90609  1.00000   0   0   0    0
              121.00   131.00   141.00  1031.00     0.00
O5   O       0.36201  0.71889  0.18555  2.90609  1.00000   0   0   0    0
              151.00   161.00   171.00  1031.00     0.00
O6   O       0.57821  0.60724  0.30151  2.90609  1.00000   0   0   0    0
              181.00   191.00   201.00   1031.00     0.00
O7   O       0.35005  0.61270  0.35933  2.90609  1.00000   0   0   0    0
              211.00   221.00   231.00  1031.00     0.00
O8   O       0.16567  0.50358  0.38857  2.90609  1.00000   0   0   0    0
              241.00   251.00   261.00  1031.00     0.00
O9   O       0.66186  0.81635  0.04394  2.90609  1.00000   0   0   0    0
              271.00   281.00   291.00  1031.00     0.00
N10  N       0.75288  0.45777  0.13838  1.58174  1.00000   0   0   0    0
              301.00   311.00   321.00  1041.00     0.00
N11  N       0.46049  0.85949  0.08242  1.58174  1.00000   0   0   0    0
              331.00   341.00   351.00  1041.00     0.00
C12  C       0.01987  0.32864  0.36337  2.86195  1.00000   0   0   0    0
              361.00   371.00   381.00   651.00     0.00
C13  C      -0.04760  0.24520  0.34562  2.86195  1.00000   0   0   0    0
              391.00   401.00   411.00   651.00     0.00
C14  C      -0.03888  0.19790  0.26857  2.86195  1.00000   0   0   0    0
              421.00   431.00   441.00   651.00     0.00
C15  C       0.03547  0.23002  0.20638  2.86195  1.00000   0   0   0    0
              451.00   461.00   471.00   651.00     0.00
C16  C       0.10846  0.31727  0.22146  2.86195  1.00000   0   0   0    0
              481.00   491.00   501.00   651.00     0.00
C17  C       0.19532  0.36556  0.15400  2.86195  1.00000   0   0   0    0
              511.00   521.00   531.00   651.00     0.00
C18  C       0.31453  0.39376  0.20113  2.86195  1.00000   0   0   0    0
              541.00   551.00   561.00   651.00     0.00
C19  C       0.41903  0.43295  0.14460  2.86195  1.00000   0   0   0    0
              571.00   581.00   591.00   651.00     0.00
C20  C       0.52797  0.48451  0.19053  2.86195  1.00000   0   0   0    0
              601.00   611.00   621.00   651.00     0.00
C21  C       0.63398  0.51058  0.12199  2.86195  1.00000   0   0   0    0
              631.00   641.00   661.00   651.00     0.00
C22  C       0.65855  0.62653  0.10963  2.86195  1.00000   0   0   0    0
              671.00   681.00   691.00   651.00     0.00
C23  C       0.56261  0.69709  0.12812  2.86195  1.00000   0   0   0    0
              701.00   711.00   721.00   651.00     0.00
C24  C       0.46096  0.67040  0.18331  2.86195  1.00000   0   0   0    0
              731.00   741.00   751.00   651.00     0.00
C25  C       0.48293  0.57570  0.24342  2.86195  1.00000   0   0   0    0
              761.00   771.00   781.00   651.00     0.00
C26  C       0.37020  0.55014  0.28988  2.86195  1.00000   0   0   0    0
              791.00   801.00   811.00   651.00     0.00
C27  C       0.28989  0.46988  0.27043  2.86195  1.00000   0   0   0    0
              821.00   831.00   841.00   651.00     0.00
C28  C       0.19187  0.44584  0.32695  2.86195  1.00000   0   0   0    0
              851.00   861.00   871.00   651.00     0.00
C29  C       0.10202  0.36889  0.30115  2.86195  1.00000   0   0   0    0
              881.00   891.00   901.00   651.00     0.00
C30  C       0.55524  0.78952  0.07658  2.86195  1.00000   0   0   0    0
              911.00   921.00   931.00   651.00     0.00
C31  C       0.21594  0.29539  0.07977  2.86195  1.00000   0   0   0    0
              941.00   951.00   961.00   651.00     0.00
C32  C       0.73501  0.34343  0.13524  2.86195  1.00000   0   0   0    0
              971.00   981.00   991.00   651.00     0.00
C33  C       0.80700  0.48587  0.22202  2.86195  1.00000   0   0   0    0
             1001.00  1011.00  1021.00   651.00     0.00
!-------> Profile Parameters for Pattern #  1
!  Scale       Shape1      Bov     Str1     Str2     Str3    Strain-Model
 0.21068E-02   0.4572   0.0000   0.0000   0.0000   0.0000       0
    11.00000     0.00     0.00     0.00     0.00     0.00
!      U        V         W          X         Y       GauSiz   LorSiz Size-Model
   0.31737  -0.12372   0.03987   0.00000   0.00000   0.00000   0.00000   0
    101.00      0.00     31.00      0.00      0.00      0.00      0.00
!     a          b         c        alpha      beta       gamma
  10.969498  12.847066  15.712444  90.000000  90.000000  90.000000
    0.00000    0.00000    0.00000    0.00000    0.00000    0.00000
!  Pref1    Pref2      Asy1     Asy2     Asy3     Asy4  
  1.00000  0.00000  0.09272  0.06000  0.00000  0.00000
     0.00     0.00     0.00     0.00     0.00     0.00
! Soft distance constraints:
O2   C12    1    0.00000    0.00000    0.00000    1.35200    0.01000
O3   C17    1    0.00000    0.00000    0.00000    1.43200    0.01000
O4   C22    1    0.00000    0.00000    0.00000    1.25900    0.01000
O5   C24    1    0.00000    0.00000    0.00000    1.23400    0.01000
O6   C25    1    0.00000    0.00000    0.00000    1.42200    0.01000
O7   C26    1    0.00000    0.00000    0.00000    1.33000    0.01000
O8   C28    1    0.00000    0.00000    0.00000    1.27600    0.01000
O9   C30    1    0.00000    0.00000    0.00000    1.31300    0.01000
N10  C21    1    0.00000    0.00000    0.00000    1.49400    0.01000
N10  C32    1    0.00000    0.00000    0.00000    1.49000    0.01000
N10  C33    1    0.00000    0.00000    0.00000    1.49100    0.01000
N11  C30    1    0.00000    0.00000    0.00000    1.30100    0.01000
C12  C13    1    0.00000    0.00000    0.00000    1.38600    0.01000
C12  C29    1    0.00000    0.00000    0.00000    1.40500    0.01000
C13  C14    1    0.00000    0.00000    0.00000    1.35700    0.01000
C14  C15    1    0.00000    0.00000    0.00000    1.39900    0.01000
C15  C16    1    0.00000    0.00000    0.00000    1.37500    0.01000
C16  C17    1    0.00000    0.00000    0.00000    1.53400    0.01000
C16  C29    1    0.00000    0.00000    0.00000    1.42200    0.01000
C17  C18    1    0.00000    0.00000    0.00000    1.54000    0.01000
C17  C31    1    0.00000    0.00000    0.00000    1.51600    0.01000
C18  C19    1    0.00000    0.00000    0.00000    1.52600    0.01000
C18  C27    1    0.00000    0.00000    0.00000    1.51200    0.01000
C19  C20    1    0.00000    0.00000    0.00000    1.53400    0.01000
C20  C21    1    0.00000    0.00000    0.00000    1.53800    0.01000
C20  C25    1    0.00000    0.00000    0.00000    1.52200    0.01000
C21  C22    1    0.00000    0.00000    0.00000    1.52200    0.01000
C22  C23    1    0.00000    0.00000    0.00000    1.40300    0.01000
C23  C24    1    0.00000    0.00000    0.00000    1.42700    0.01000
C23  C30    1    0.00000    0.00000    0.00000    1.43500    0.01000
C24  C25    1    0.00000    0.00000    0.00000    1.55200    0.01000
C25  C26    1    0.00000    0.00000    0.00000    1.50800    0.01000
C26  C27    1    0.00000    0.00000    0.00000    1.35400    0.01000
C27  C28    1    0.00000    0.00000    0.00000    1.44500    0.01000
C28  C29    1    0.00000    0.00000    0.00000    1.45100    0.01000

Restrained Refinement in Fullprof

The Fullprof *.out output file will tell you what is going on with respect to the bond length restraints and if you have made any obvious mistakes setting things up.

 => Distance constraints:      Dobs     Dcalc  diff/sigma
    (O2   - C12 ):          1.35200   1.33918     1.28200
    (O3   - C17 ):          1.43200   1.44425    -1.22492
    (O4   - C22 ):          1.25900   1.25923    -0.02342
    (O5   - C24 ):          1.23400   1.27322    -3.92196
    (O6   - C25 ):          1.42200   1.44513    -2.31262
    (O7   - C26 ):          1.33000   1.37402    -4.40164
    (O8   - C28 ):          1.27600   1.29485    -1.88483
    (O9   - C30 ):          1.31300   1.32626    -1.32631
    (N10  - C21 ):          1.49400   1.49864    -0.46387
    (N10  - C32 ):          1.49000   1.48344     0.65643
    (N10  - C33 ):          1.49100   1.46163     2.93682
    (N11  - C30 ):          1.30100   1.34755    -4.65486
    (C12  - C13 ):          1.38600   1.37961     0.63871
    (C12  - C29 ):          1.40500   1.43496    -2.99565
    (C13  - C14 ):          1.35700   1.35754    -0.05361
    (C14  - C15 ):          1.39900   1.41365    -1.46538
    (C15  - C16 ):          1.37500   1.39229    -1.72884
    (C16  - C17 ):          1.53400   1.54902    -1.50199
    (C16  - C29 ):          1.42200   1.45817    -3.61701
    (C17  - C18 ):          1.54000   1.52876     1.12411
    (C17  - C31 ):          1.51600   1.49568     2.03242
    (C18  - C19 ):          1.52600   1.53847    -1.24725
    (C18  - C27 ):          1.51200   1.54576    -3.37646
    (C19  - C20 ):          1.53400   1.52490     0.90995
    (C20  - C21 ):          1.53800   1.54776    -0.97597
    (C20  - C25 ):          1.52200   1.56787    -4.58719
    (C21  - C22 ):          1.52200   1.55911    -3.71107
    (C22  - C23 ):          1.40300   1.44134    -3.83443
    (C23  - C24 ):          1.42700   1.48698    -5.99785
    (C23  - C30 ):          1.43500   1.47896    -4.39645
    (C24  - C25 ):          1.55200   1.58359    -3.15930
    (C25  - C26 ):          1.50800   1.53789    -2.98923
    (C26  - C27 ):          1.35400   1.41101    -5.70073
    (C27  - C28 ):          1.44500   1.46845    -2.34495
    (C28  - C29 ):          1.45100   1.47536    -2.43574

GSAS GUI WINORTEP by Louis Farrugia to examine the Structure and resulting bond lengths and angles during the refinement

Using Ortep-3 you can quickly load the Fullprof *.pcr file and check that the bond length and angle restraints are doing what you think they should be doing (using the Calculate menu option). You can also keep a graphical eye on the thermals.

Ortep-3 - http://www.chem.gla.ac.uk/~louis/software/ortep3/ | [CCP14 UK Mirror | CCP14 Australian Mirror | CCP14 Canadian Mirror]

In the following case, thermals are quite large, possibly due to poorly defined manual background. Switching to a refined background might be a better thing to do here.

Ortep-3 with a Fullprof pcr structure file

Looking at the Rietveld plot in Winplotr

Examining the Rietveld plot in Winplotr

Further Options

You may want to re-import the structure back into Crystals (using Ortep-3) to allow very easy placement of hydrogens (Structure, Add Hydrogens); as well as possible validation with the CSD database to check that bond-length and angles are consistent with structures already in the Cambridge Database.

A "might happen" feature for a future version of Crystals is to generate idealised bond lengths and bond angles based on the cambridge database in a similar way to how Crystals presently does the CSD validation.

[Back to Problems and Solutions] | [Back to Restrained Rietveld Refinement of Organics Page]| [Back to Fullprof Tutorials Page]

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